Charred rice grain, that were excavated from archaeological sites were used in this study. The rice grains used here were mainly collected by the late Mr. Toshiya Sato, who has been actively studying on the shape of rice grains excavated during 1960s to 1985. The samples have been preserved in Osaka prefecture Yayoi culture Museum.The samples were first taken their photos under the CCD microscopic camera. The data has been kept as digital records. The size of the data was as big as 1.5 Mb to 2.0 Mb. The records will be taken into a database with the archaeological records as well as the data for their shape and size.Then, DNA analysis was performed to know their genetic feature. DNA was extracted by alkaline SDS method. DNA Extracted was amplified by PCR to know whether the rice was classified into indica or japonica, and if japonica, temperate japonica or tropical japonica. The results showed that almost all samples belonged to japonica. Some belonged to tropical japonica, that adapts to extensive cultivation. Perhaps, ancient rice cultivation in Japan islands showed a similarity to slash-and-burn system, which is performed in upland areas in Indochina peninsula still now.